[English] 日本語
Yorodumi- PDB-5amx: Crystal Structure of Proteinase K processed with the CrystalDirec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5amx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Proteinase K processed with the CrystalDirect automated mounting and cryo-cooling technology | ||||||
Components | PROTEINASE K | ||||||
Keywords | HYDROLASE / PROTEINASE / AUTOMATED CRYSTAL HARVESTING / AUTOMATED CRYO-COOLING / CRYSTALDIRECT | ||||||
Function / homology | Function and homology information peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ENGYODONTIUM ALBUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.01 Å | ||||||
Authors | Zander, U. / Hoffmann, G. / Cornaciu, I. / Cipriani, F. / Marquez, J.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2016 Title: Automated Harvesting and Processing of Protein Crystals Through Laser Photoablation. Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / ...Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / Mathieu, M. / Cipriani, F. / Marquez, J.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5amx.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5amx.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 5amx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5amx_validation.pdf.gz | 433.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5amx_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 5amx_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 5amx_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/5amx ftp://data.pdbj.org/pub/pdb/validation_reports/am/5amx | HTTPS FTP |
-Related structure data
Related structure data | 5amwC 5amzC 5an4C 5andC 5aneC 5angC 5aniC 5anjC 5ankC 5anlC 5anoC 5dwpC 5ebhC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28930.783 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 106-384 / Source method: isolated from a natural source / Source: (natural) ENGYODONTIUM ALBUM (fungus) / References: UniProt: P06873, peptidase K |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.63 % / Description: NONE |
---|---|
Crystal grow | Details: 0.1 M HEPES, PH=7.5, 1.3 M AMMONIUM SULFATE, 0.1 M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.01→30 Å / Num. obs: 113538 / % possible obs: 89.6 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.05 |
-Processing
Software | Name: REFMAC / Version: 5.8.0123 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.01→29.13 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.326 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES, REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.249 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.01→29.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|